The document discusses the NIH's vision of becoming a digital enterprise to enhance biomedical research. It outlines how research is becoming more digital and data-driven. The NIH aims to foster open sharing of data and tools through its Commons platform to facilitate collaboration and reproducibility. It also stresses the importance of training the next generation of data scientists to enable the digital enterprise. The end goal is to accelerate discovery and improve health outcomes through more integrated and data-driven research.
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
RDAP 15 EarthCollab: Connecting Scientific Information Sources using the Sema...ASIS&T
Research Data Access and Preservation Summit, 2015
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April 22-23, 2015
Erica M. Johns, Jon Corson-Rikert, Huda J. Khan, Dean B. Krafft and Matthew S. Mayernik
NITRD Big Data Interagency Working Group Workshop: Pioneering the Future of Federally Supported Data Repositories Jan 13, 2021 - Opening comments on where we are and one suggestion of where we might go with an International Data Science Institute (IDSI) - A blue sky view.
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
RDAP 15 EarthCollab: Connecting Scientific Information Sources using the Sema...ASIS&T
Research Data Access and Preservation Summit, 2015
Minneapolis, MN
April 22-23, 2015
Erica M. Johns, Jon Corson-Rikert, Huda J. Khan, Dean B. Krafft and Matthew S. Mayernik
NITRD Big Data Interagency Working Group Workshop: Pioneering the Future of Federally Supported Data Repositories Jan 13, 2021 - Opening comments on where we are and one suggestion of where we might go with an International Data Science Institute (IDSI) - A blue sky view.
Poster RDAP13: Data information literacy multiple paths to a single goalASIS&T
Jake Carlson, Jon Jeffryes, Brian Westra and Sarah Wright
Data Information Literacy: Multiple Paths to a Single Goal
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
The goal of the Very Open Data Project is to provide a software-technical foundation for this exchange of data, more specifically to provide an open database platform for data from the raw data coming from experimental measurements or models through intermediate manipulations to finally published results. The sheer expanse of the amount data involved creates some unique software-technical challenges. One of these challenges is addressed in the part of the study presented here, namely to characterize scientific data (with the initial focus being detailed chemistry data from the combustion kinetic community), so that efficient searches can be made. A formalization of this characterization comes in the form of schemas of descriptions of tags and keywords describing data and ontologies describing the relationship between data types and the relationship between the characterizations themselves. These will be translated to meta-data tags connected to the data points within a non-relational data of data for the community.
The focus of the initial work will be on data and its accessibility. As the project progresses, the emphasis will shift on not only having available data accessible for the community, but that the community itself will be able to, with emphasis on minimal effort, will be able contribute their own data. This will involve, for example, the concepts of the ‘electronic lab notebook’ and the existence and availability of extensive concept extraction tools, primarily from the chemical informatics field.
Information technology and resources are an integral and indispensable part of the contemporary academic enterprise. In particular, technological advances have nurtured a new paradigm of data-intensive research. However, far too much of this activity still takes place in silos, to the detriment of open scholarly inquiry, integrity, and advancement. To counteract this tendency, the University of California Curation Center (UC3) has been developing and deploying a comprehensive suite of curation services that facilitate widespread data management, preservation, publication, sharing, and reuse. Through these services UC3 is engaging with new communities of use: in addition to its traditional stakeholders in cultural heritage memory organizations, e.g., libraries, museums, and archives, the UC3 service suite is now attracting significant adoption by research projects, laboratories, and individual faculty researchers. This webinar will present an introduction to five specific services – DMPTool, DataUp, EZID, Merritt, Web Archiving Service (WAS) – applicable to data curation throughout the scholarly lifecycle, two recent initiatives in collaboration with UC campuses, UC Berkeley Research Hub and UC San Francisco DataShare, and the ways in which they encourage and promote new communities of practice and greater transparency in scholarly research.
Poster RDAP13: A Workflow for Depositing to a Research Data Repository: A Cas...ASIS&T
Betsy Gunia, David Fearon, Benjamin Brosius, Tim DiLauro
JHU Data Management Services
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A Workflow for Depositing to a Research Data Repository: A Case Study for Archiving Publication Data
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Poster RDAP13: Research Data in eCommons @ Cornell: Present and FutureASIS&T
Wendy A. Kozlowski, Dianne Dietrich, Gail Steinhart and Sarah Wright
Cornell University Library, Ithaca, NY
Research Data in eCommons @ Cornell: Present and Future
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Feb 26 NISO Training Thursday
Crafting a Scientific Data Management Plan
About the Training
Addressing a data management plan for the first time can be an intimidating exercise. Join NISO for a hands-on workshop that will guide you through the elements of creating a data management plan, including gathering necessary information, identifying needed resources, and navigating potential pitfalls. Participants explore the important components of a data management plan and critique excerpts of sample plans provided by the instructors.
This session is meant to be a guided, step-by-step session that will follow the February 18 NISO Virtual Conference, Scientific Data Management: Caring for Your Institution and its Intellectual Wealth.
About the Instructors
Kiyomi D. Deards, MSLIS, Assistant Professor, University of Nebraska-Lincoln Libraries
Jennifer Thoegersen, Data Curation Librarian, University of Nebraska-Lincoln Libraries
Poster RDAP13: Data information literacy multiple paths to a single goalASIS&T
Jake Carlson, Jon Jeffryes, Brian Westra and Sarah Wright
Data Information Literacy: Multiple Paths to a Single Goal
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
The goal of the Very Open Data Project is to provide a software-technical foundation for this exchange of data, more specifically to provide an open database platform for data from the raw data coming from experimental measurements or models through intermediate manipulations to finally published results. The sheer expanse of the amount data involved creates some unique software-technical challenges. One of these challenges is addressed in the part of the study presented here, namely to characterize scientific data (with the initial focus being detailed chemistry data from the combustion kinetic community), so that efficient searches can be made. A formalization of this characterization comes in the form of schemas of descriptions of tags and keywords describing data and ontologies describing the relationship between data types and the relationship between the characterizations themselves. These will be translated to meta-data tags connected to the data points within a non-relational data of data for the community.
The focus of the initial work will be on data and its accessibility. As the project progresses, the emphasis will shift on not only having available data accessible for the community, but that the community itself will be able to, with emphasis on minimal effort, will be able contribute their own data. This will involve, for example, the concepts of the ‘electronic lab notebook’ and the existence and availability of extensive concept extraction tools, primarily from the chemical informatics field.
Information technology and resources are an integral and indispensable part of the contemporary academic enterprise. In particular, technological advances have nurtured a new paradigm of data-intensive research. However, far too much of this activity still takes place in silos, to the detriment of open scholarly inquiry, integrity, and advancement. To counteract this tendency, the University of California Curation Center (UC3) has been developing and deploying a comprehensive suite of curation services that facilitate widespread data management, preservation, publication, sharing, and reuse. Through these services UC3 is engaging with new communities of use: in addition to its traditional stakeholders in cultural heritage memory organizations, e.g., libraries, museums, and archives, the UC3 service suite is now attracting significant adoption by research projects, laboratories, and individual faculty researchers. This webinar will present an introduction to five specific services – DMPTool, DataUp, EZID, Merritt, Web Archiving Service (WAS) – applicable to data curation throughout the scholarly lifecycle, two recent initiatives in collaboration with UC campuses, UC Berkeley Research Hub and UC San Francisco DataShare, and the ways in which they encourage and promote new communities of practice and greater transparency in scholarly research.
Poster RDAP13: A Workflow for Depositing to a Research Data Repository: A Cas...ASIS&T
Betsy Gunia, David Fearon, Benjamin Brosius, Tim DiLauro
JHU Data Management Services
Johns Hopkins University Sheridan Libraries
A Workflow for Depositing to a Research Data Repository: A Case Study for Archiving Publication Data
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Poster RDAP13: Research Data in eCommons @ Cornell: Present and FutureASIS&T
Wendy A. Kozlowski, Dianne Dietrich, Gail Steinhart and Sarah Wright
Cornell University Library, Ithaca, NY
Research Data in eCommons @ Cornell: Present and Future
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Feb 26 NISO Training Thursday
Crafting a Scientific Data Management Plan
About the Training
Addressing a data management plan for the first time can be an intimidating exercise. Join NISO for a hands-on workshop that will guide you through the elements of creating a data management plan, including gathering necessary information, identifying needed resources, and navigating potential pitfalls. Participants explore the important components of a data management plan and critique excerpts of sample plans provided by the instructors.
This session is meant to be a guided, step-by-step session that will follow the February 18 NISO Virtual Conference, Scientific Data Management: Caring for Your Institution and its Intellectual Wealth.
About the Instructors
Kiyomi D. Deards, MSLIS, Assistant Professor, University of Nebraska-Lincoln Libraries
Jennifer Thoegersen, Data Curation Librarian, University of Nebraska-Lincoln Libraries
PSB2014 A Vision for Biomedical ResearchPhilip Bourne
Some preliminary thoughts about my role as Associate Director for Data Science at the NIH so as to have a discussion with attendees at the Pacific Symposium on Biocomputing on Jan 4, 2014, The Big Island of Hawaii.
Funding agencies are instituting requirements for data management and sharing as a condition of receiving research funds. This presentation addresses why researchers should care about research data management, what libraries have to do with it, and a case study of what one research specialist at the University of Colorado Anschutz Medical Campus is doing in this area.
Similar to The NIH as a Digital Enterprise: Implications for PAG (20)
Presented online as part of the NASM series in Advancing Drug Discovery see https://www.nationalacademies.org/event/40883_09-2023_advancing-drug-discovery-data-science-meets-drug-discovery
For a panel discussion at the Associate Research Libraries Spring meeting April 27, 2022, Montreal https://www.arl.org/schedule-for-spring-2022-association-meeting/
Frontiers of Computing at the Cellular and Molecular ScalesPhilip Bourne
3 basic points when establishing a new biomedical initiative. Presented at Frontiers of Computing in Health and Society, George Mason University, September 21, 2021.
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The NIH as a Digital Enterprise: Implications for PAG
1. The NIH as a Digital Enterprise:
Implications for PAG
Philip E. Bourne, PhD
Associate Director for Data Science
National Institutes of Health
PAG San Diego
January 11, 2015
2. What do we mean by the notion of a
Digital Enterprise?
8. And This May Just be the Beginning
Evidence:
– Google car
– 3D printers
– Waze
– Robotics
From: The Second Machine Age: Work, Progress,
and Prosperity in a Time of Brilliant Technologies
by Erik Brynjolfsson & Andrew McAfee
11. ADDS Mission
Statement
To foster an open ecosystem that
enables biomedical* research to be
conducted as a digital enterprise that
enhances health, lengthens life and
reduces illness and disability
* Includes biological, biomedical, behavioral, social,
environmental, and clinical studies that relate to understanding
health and disease.
12. Some Goals of the Digital Enterprise
Cost savings through sharing of best
practices
Sustainability of digital assets
Collaboration through identification of
collaborators at the point of data collection
not publication
Improved reproducibility through data and
methods sharing
Integration of data types and data and
literature to accelerate discovery
13. Some of Today’s Observations
Bad News
– We do not yet have a
data sustainability plan
– Global policies define the
why but not the how
– We do not know how all
the data we currently
have are used
– We can’t estimate future
supply and demand
– We need to ramp up
training programs in data
science
Good news
– Genuine willingness to
address the problem
– Global communities are
emerging
– Efficiencies can be
achieved
– BD2K is the beginnings
of a plan
– We are beginning to
quantify the issues
15. What is the NIH Doing to Fulfill
That Promise?
16. Elements of The Digital Enterprise
Community
Policy
Infrastructure
• Sustainability
• Collaboration
• Training
17. Elements of The Digital Enterprise
Community
Policy
Infrastructure
• Sustainability
Collaboration
• Training
Virtuous
Research
Cycle
18. Policies – Now & Forthcoming
Data Sharing
– Genomic data sharing announced
– Data sharing plans on all research awards
– Data sharing plan enforcement
• Machine readable plan
• Repository requirements to include grant numbers
http://www.nih.gov/news/health/aug2014/od-27.htm
19. Policies - Forthcoming
Data Citation
– Goal: legitimize data as a form of scholarship
– Process:
• Machine readable standard for data citation (done)
• Endorsement of data citation for inclusion in NIH bib
sketch, grants, reports, etc.
• Example formats for human readable data citations
• Slowly work into NLM/NCBI workflow
22. The Commons: Compute Platforms
The Commons
Conceptual Framework
Public Cloud
Platforms
Super Computing
(HPC) Platforms
Other
Platforms ?
Google, AWS (Amazon)
Microsoft (Azure), IBM,
other?
In house compute
solutions
Private clouds, HPC
– Pharma
– The Broad
– Bionimbus
Traditionally low access
by NIH
24. How Might PAG’s Participate?
Consider contributing digital research objects into the
Commons – data, software, standards, narrative,
course materials …
Initiate your own moves from cylinders of excellence
to more integrated and multi-functional data sources
Work to define new business models for the scientific
enterprise
26. Generic Needs
Homogenization of disparate large unstructured
datasets
Deriving structure from unstructured data
Feature mapping and comparison from image data
Visualization and analysis of multi-dimensional
phenotypic datasets
Causal modeling of large scale dynamic networks
and subsequent discovery
Utilize data that are sparsely and irregularly sampled
and noisy
BD2K will offer reference datasets and points of
domain expertise to explore these questions
27. 1) Build an OPEN digital framework for data
science training:
NIH Data Science Workforce Development Center
1) Develop short-term training opportunities:
Courses, educational resources, etc.
1) Develop the discipline of biomedical data
science and support cross-training – OPEN
courseware
Community: Training
Data Science Training Goals
All goals have a diversity component and manate
28. Associate Director for Data Science
Commons BD2K Efficiency
Sustainability Education Innovation Process
• Cloud – Data &
Compute
• Search
• Security
• Reproducibility
Standards
• App Store
• Coordinate
• Hands-on
• Syllabus
• MOOCs
• Community
• Centers
• Training Grants
• Catalogs
• Standards
• Analysis
• Data
Resource
Support
• Metrics
• Best
Practices
• Evaluation
• Portfolio
Analysis
The Biomedical Research Digital Enterprise
Partnerships
Collaboration
rogrammatic Theme
Deliverable
Example Features • IC’s
• Researchers
• Federal
Agencies
• International
Partners
• Computer
Scientists
Scientific Data Council External Advisory Board
Training
30. Potential Outcomes
Mobility: improve the outcomes of surgeries in
children with cerebral palsy and gait pathology
Wellness: markers derived from constantly monitored
eHealth/mobile health devices – apply to smoking
cessation, weight loss
Cancer: further personalization of treatment
Mental Health: better identify factors that resist and
promote brain disease e.g., schizophrenia, bipolar
disorder, major depression, attention deficit
hyperactivity disorder (ADHD), obsessive compulsive
disorder (OCD), autism
Addiction: utilizing social media to track and treat
drug use and addiction
Editor's Notes
Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med 2(8): e124. doi:10.1371/journal.pmed.0020124
http://www.reuters.com/article/2012/03/28/us-science-cancer-idUSBRE82R12P20120328